Of course it's a collaboration. For Pete's sake people, Ninja Gaiden is it's own IP. Only difference is that it simply lives in the same building as you. It's merely your neighbor.
I guess to make it seem more like a guest appearance for those new to DOA. It's kinda funny how Kasumi and everyone seems to be surprised/honored that Momiji fights them even tho she was nothing special in DOA5U
Same with Namco's Soul Calibur and Tekken. Same building, but not exactly tied at all. When Heihachi entered Soul Calibur, he was considered as a guest character by Okubo himself.